Table 2.
Primers and probes.
| Method | Name | Sequence | Length | Positiona | Product | Reference |
|---|---|---|---|---|---|---|
| hnRT-PCR | JW12-F | ATGTAACACCYCTACAATG | 19 | 55–73 | Panning et al., 2010 [22] | |
| JW6AS1-R1 | CAATTGGCACACATTTTGTG | 20 | 660–641 | 606 bp | ||
| JW6AS2-R1 | CAGTTAGCGCACATCTTATG | 20 | 660–641 | 606 bp | ||
| JW10AS1-R2 | GTCATCAATGTGTGATGTTC | 20 | 636–617 | 582 bp | ||
| JW10AS2-R2 | GTCATTAGAGTATGGTGCTC | 20 | 636–617 | 582 bp | ||
|
| ||||||
| Cloning RT-PCR | TWclon-F | ACGCTTAACRACMAAACCAG | 20 | 1–20 | This work | |
| TWclon-R | TGKATGAARTAAGAGTGWGGRAC | 23 | 933–911 | 933 bp | ||
|
| ||||||
| Control1 | GAPDH-F | GGCAAGTTCCATGGCACAGT | 20 | 58–72b | Ravazzolo et al., 2006 [37] | |
| GAPDH-R | ACGTACTCAGCACCAGCATCAC | 22 | 161–182b | 125 bp | ||
|
| ||||||
| Real-time RT-PCR | RABVD1-F | ATGTAACACCYCTACAATG | 19 | 55–73 | Nadin-Davis et al., 2009 [8] | |
| RABVD1-R | GCMGGRTAYTTRTAYTCATA | 20 | 165–146 | 111 bp | Nadin-Davis et al., 2009 [8] | |
| RABVD1-P | 5′-FAM-CCGAYAAGATTGTATTYAARGTCAAKAATCAGGT-BHQ1-3′ | 34 | 78–111 | Nadin-Davis et al., 2009 [8] | ||
| LysGT5-P | 5′-YY-AACARGGTTGTTTTYAAGGTCCATAA-BHQ1-3′ | 26 | 80–105 | Wakeley et al., 2005 [25] | ||
| LysGT6-P | 5′-Cy5-ACARAATTGTCTTCAARGTCCATAATCAG-BHQ2-3′ | 29 | 81–109 | Wakeley et al., 2005 [25] | ||
| ivvWCBV-P | 5′-FAM-TCGGATATCACTTCGGGTTTGAGAGTCA-BHQ1-3′ | 28 | 141–114 | This work | ||
| ivvMok-P | 5′-YY-TTGTGTTCAAGGTGAAYAAYCAAGT-BHQ1-3′ | 25 | 87–111 | This work | ||
| ivvABLV2n-P | 5′Cy5-ATTGTCTTTAAGGTCAACAATCAGTT-BHQ2-3′ | 26 | 86–111 | This work | ||
| ivvLBV-P | 5′-FAM-ATTGTTTTCAAAGTYCAYAATCAGGTMGTGTC-BHQ1-3′ | 32 | 86–117 | This work | ||
| ivvKhujand-P | 5′-YY-ACAGAATTGTCTTYAAAGTYMAKAATCA-BHQ1-3′ | 28 | 81–108 | This work | ||
| ivvSBLV2-P | 5′-Cy5-TCWGAGATTATRTCTGGCTTCAAAGACAC-BHQ2-3′ | 29 | 141–113 | This work | ||
|
| ||||||
| Control1 | Sendai-F | GTCATGGATGGGCAGGAGTC | 20 | 8553–8572b | Kaiser, 2001 [38] | |
| Sendai-R | CGTTGAAGAGCCTTACCCAGA | 21 | 8788–8768b | 236 bp | ||
| Sendai-P | 5′-FAM-CAAAATTAGGAACGGAGGATTGTCCCCTC-Tamra-3′ | 29 | 8720–8748b | |||
Changed bases referring to the reference are underlined. Wobbled positions are as follows: Y = C/T, X/N = G/A/T/C, W = A/T, S = C/G, R = A/G, M = A/C, K = G/T, H = A/C/T, and B = C/G/T.
aRabies primer and probe positions are given according to the Pasteur virus genome (accession number X03673).
bPositions of the GAPDH-primers refer to the GenBank sequence AJ431207; positions of the Sendai-primers refer to the GenBank sequence M30202.
1Controls for classical and real-time RT-PCR.
FAM: 6-carboxyfluorescein reporter dye, BHQ-1: Black Hole Quencher-1, YY: Yakima Yellow, Cy5: Cyanine 5, BHQ-2: Black Hole Quencher-2, and Tamra: carboxy-tetramethyl-rhodamine.